Workflow

Click the nodes to obtain details about each step.

Mosaic counts

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

Configuration files
File Code
config/config.yaml 
  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
mode: "count"
plot: False
check_sm_tag_in_bam_header: "False"

config_df_location: "config/config_df.tsv"

# Input BAM location
input_bam_ena: "/g/korbel2/weber/MosaiCatcher_files/bam_KG_full/"
input_bam_location: "/g/korbel2/weber/MosaiCatcher_files/bam_KG_full/"

output_location: "/g/korbel2/weber/MosaiCatcher_output/MosaiCatcher_output_sample_KG_dryrun/"
snv_sites_to_genotype: "/g/korbel2/weber/MosaiCatcher_files/snv_sites_to_genotype/ALL.chr1-22plusX_GRCh38_sites.20170504.renamedCHR.vcf.gz"
# FIXME : TMP debuging
# snv_sites_to_genotype: "/g/korbel2/weber/MosaiCatcher_files/snv_sites_to_genotype/split_by_chr/1000G_chr21.vcf.gz"

reference: "/g/korbel2/weber/MosaiCatcher_files/refgenomes_human_local/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
# reference: "/g/korbel2/weber/MosaiCatcher_files/refgenomes_human_local/chr21.fna"

# TODO : add a SMK rule to clone & compile mosaic
mosaicatcher: "/g/korbel2/weber/Gits/mosaicatcher/build/mosaic"

# FIXME : TMP solution for strandphaser location
strandphaser: "/home/tweber/.conda/envs/strandseqnation/lib/R/library/StrandPhaseR/R/StrandPhaseR"
Rscript: "/home/tweber/.conda/envs/strandseqnation/bin/Rscript"

# TODO : remove hard coded paths for R scripts coming from MC
plot_script: "/g/korbel2/weber/Gits/mosaicatcher/R/qc.R"
sv_plot_script: "/g/korbel2/weber/Gits/mosaicatcher/R/chrom.R"
norm_script: "/g/korbel2/weber/Gits/mosaicatcher/R/norm.R"

# CHECKME : check implicit natural path through Conda env
samtools: "/g/funcgen/bin/samtools"
# bcftools: "/biolo/ngs/bin/bcftools"

# TODO : path reference
variable_bins:
  "50000": "/g/korbel2/weber/workspace/pipeline/utils/variable_bins.GRCh38.50kb.bed"
  "100000": "/g/korbel2/weber/workspace/pipeline/utils/variable_bins.GRCh38.100kb.bed"

# TODO : find another solution with conda for R_ref
R_reference: "BSgenome.Hsapiens.UCSC.hg38"

# CHECKME : Parameters optimization ?

exclude_list:
  - BM510x3PE20490

chromosomes:
  - chr21

# chromosomes:
#   - chr1
#   - chr2
#   - chr3
#   - chr4
#   - chr5
#   - chr6
#   - chr7
#   - chr8
#   - chr9
#   - chr10
#   - chr11
#   - chr12
#   - chr13
#   - chr14
#   - chr15
#   - chr16
#   - chr17
#   - chr18
#   - chr19
#   - chr20
#   - chr21
#   - chr22
#   - chrX

# Parameters
## WINDOW
window: 100000

## METHODS

llr: 4
poppriors: TRUE
haplotags:
  - TRUE
  - FALSE
gtcutoff:
  - 0
  - 0.05
regfactor: 6
filter:
  - TRUE
  - FALSE

## BPDENS
### JOINT SEG
min_diff_jointseg: 0.1
### SINGLE SEG
min_diff_singleseg: 0.5
### SCE CUTOFF
additional_sce_cutoff: 20000000
### SCE MIN DISTANCE
sce_min_distance: 500000

Loading...